Freshwater lakes are an important component of the global carbon cycle through both organic carbon (OC) sequestration and carbon dioxide (CO₂) emission. Most lakes have a net annual loss of CO₂ to the atmosphere and substantial current evidence suggests thatbiologic mineralization of allochthonous OC maintains this flux. Because net CO₂ flux to the atmosphere implies net mineralization of OC within the lake ecosystem, it is also commonly assumed that net annual CO₂ emission indicates negative net ecosystem production (NEP). We explored the relationship between atmospheric CO₂ emission and NEP in two lakes known to have contrasting hydrologic characteristics and net CO₂ emission. We calculated NEP for calendar year 2004 using whole-lake OC and inorganic carbon (IC) budgets, NEP_OC and NEP_IC, respectively, and compared the resulting values to measured annual CO₂ flux from the lakes. In both lakes, NEP_OC and NEP_IC were positive, indicating net autotrophy. Therefore CO₂ emission from these lakes was apparently not supported by mineralization of allochthonous organic material. In both lakes, hydrologic CO₂ inputs, as well as CO₂ evolved from net calcite precipitation, could account for the net CO₂ emission. NEP calculated from diel CO₂ measurements was also affected by hydrologic inputs of CO₂. These results indicate that CO₂ emission and positive NEP may coincide in lakes, especially in carbonate terrain, and that all potential geologic, biogeochemical, and hydrologic sources of CO₂ need to be accounted for when using CO₂ concentrations to infer lake NEP.